plasmidSPAdes: assembling plasmids from whole genome sequencing data

Plasmids are stably maintained extra-chromosomal genetic elements that replicate independently from the host cell's chromosomes. Although plasmids harbor biomedically important genes, (such as genes involved in virulence and antibiotics resistance), there is a shortage of specialized software t...

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Published in:Bioinformatics (Oxford, England) England), 2016-11, Vol.32 (22), p.3380-3387
Main Authors: Antipov, Dmitry, Hartwick, Nolan, Shen, Max, Raiko, Mikhail, Lapidus, Alla, Pevzner, Pavel A
Format: Article
Language:English
Subjects:
Algorithms
Genome, Bacterial
Plasmids - genetics
Sequence Analysis, DNA
Software
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description Plasmids are stably maintained extra-chromosomal genetic elements that replicate independently from the host cell's chromosomes. Although plasmids harbor biomedically important genes, (such as genes involved in virulence and antibiotics resistance), there is a shortage of specialized software tools for extracting and assembling plasmid data from whole genome sequencing projects. We present the plasmidSPAdes algorithm and software tool for assembling plasmids from whole genome sequencing data and benchmark its performance on a diverse set of bacterial genomes. plasmidSPAdes is publicly available at http://spades.bioinf.spbau.ru/plasmidSPAdes/ CONTACT: d.antipov@spbu.ruSupplementary information: Supplementary data are available at Bioinformatics online.
doi_str_mv 10.1093/bioinformatics/btw493
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subjects Algorithms
Genome, Bacterial
Plasmids - genetics
Sequence Analysis, DNA
Software
title plasmidSPAdes: assembling plasmids from whole genome sequencing data
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